The spill, caused by a sewer failure in Llanberis, entered the lake via the Afon Goch polluting the bottom 30 metres of the stream.
A serious sewage spill is being investigated by officials at a Snowdonia mountain lake.
The Environment Agency said the untreated sewage entered Llyn Padarn in Llanberis, Gwynedd, after a sewer failure.
The sewage went into the lake via the Afon Goch. The damage to the lake and the river it feeds, the Afon Seiont, is being assessed.
The lake was affected by a toxic algal bloom last year.
The Environment Agency said the sewer had been repaired and there were no further leaks, although it was not known how much sewage had spilled into the lake.
David Edwell, North Wales manager for Environment Agency Wales, said: "We were contacted by a member of the public at 10am this morning and we rushed to the scene.
"We believe it had been going on for quite some time.
"We have now launched an official investigation into this incident to find out how it happened, how it could have been avoided and how much damage it has caused.
"It is disappointing as this lake in particular is highly sensitive to the effects of sewage pollution and this certainly does not help."
The Countryside Council for Wales, Gwynedd Council and the local angling club have been informed.
The Environment Agency is investigating a serious sewage spill in Llanberis
In a statement Dwr Cymru Welsh Water, which owns the treatment works, said it was alerted to the "pollution incident" on Wednesday morning and a team was immediately dispatched to investigate.
"The team are still on site and there are no discharges into the lake at present but we will continue to monitor the situation carefully and work closely with Environment Agency Wales," it added.
Earlier this month, a report showed that a "perfect storm" of nutrients from sewage effluent and unusual weather conditions was the cause of toxic algae on the lake in 2009.
It had been closed to leisure users for much of last summer and local businesses said their trade had been affected.
The report commissioned by the Environment Agency called for stricter limits on effluent discharged from the local sewage treatment works.
Huw Hughes, the secretary of the Seiont, Gwyrfai, Llyfni Angling Association, said the situation at Llanberis was "completely unacceptable".
"Put simply the sewage system is archaic, and the pipe which broke was a cast iron one, and that kind of pipe should have been replaced," he said.
Mr Hughes said he had visited the lake to see for himself what was going on.
He added the sewage was still going into the river in the middle of the afternoon, but workers were trying to isolate the flow.
"Workmen were alerted to it at seven o'clock this morning so God knows when it started," he said.
"It's completely incredible, and it's not fair on the people of Llanberis either.
"There were people there walking their dogs and canoeists on the water - they probably did not realise what was going on," he added.